JSON refactoring

[jalview.git] / src / jalview / urls / IdentifiersUrlProvider.java

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index f32e590..0dab719 100644 (file)
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -25,20 +25,18 @@ import static jalview.util.UrlConstants.DB_ACCESSION;
 import static jalview.util.UrlConstants.DELIM;
 import static jalview.util.UrlConstants.SEP;
 
+import jalview.util.JSONUtils;
 import jalview.util.UrlLink;
 
-import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
 /**
@@ -76,19 +74,20 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
    *          name of identifiers.org download file
    * @return hashmap of identifiers.org data, keyed by MIRIAM id
    */
-  private HashMap<String, UrlLink> readIdentifiers(String idFileName)
+  @SuppressWarnings("unchecked")
+private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   {
-    JSONParser parser = new JSONParser();
-
     // identifiers.org data
     HashMap<String, UrlLink> idData = new HashMap<String, UrlLink>();
 
     String errorMessage = null;
     try
     {
+       // NOTE: THIS WILL FAIL IN SWINGJS BECAUSE IT INVOLVES A FILE READER
+    
       FileReader reader = new FileReader(idFileName);
       String key = "";
-      JSONObject obj = (JSONObject) parser.parse(reader);
+      Map<String, Object> obj = (Map<String, Object>) JSONUtils.parse(reader);
       if (obj.containsKey(ID_ORG_KEY))
       {
         key = ID_ORG_KEY;
@@ -104,12 +103,12 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
         return idData;
       }
 
-      JSONArray jsonarray = (JSONArray) obj.get(key);
+      List<Object> jsonarray = (List<Object>) obj.get(key);
 
       // loop over each entry in JSON array and build HashMap entry
       for (int i = 0; i < jsonarray.size(); i++)
       {
-        JSONObject item = (JSONObject) jsonarray.get(i);
+        Map<String, Object> item = (Map<String, Object>) jsonarray.get(i);
 
         String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
                 + DELIM;